Surat police had booked Sai under various IPC sections including rape, unnatural sex, molestation, wrongful confinement, unlawful assembly, rioting with deadly weapons, criminal intimidation and criminal conspiracy.
In her complaint, the younger of the two sisters had accused Sai of repeated sexual assaults between 2002 and 2005 when she lived at his Surat ashram.
The elder sister, in her complaint against Asaram, had accused him of repeated sexual assaults between 1997 and 2006 when she lived at his ashram on the outskirts of Ahmedabad.
The complaint against Asaram, which was initially lodged at Surat's Jehangirpura police station, was transferred to Ahmedabad's Chandkheda police station, since the alleged incident took place there.
Asaram (72) is currently lodged in Jodhpur jail after being arrested in September for alleged sexual assault on a minor girl at his Jodhpur ashram.